Install¶

The easiest way to install abstar locally (on OSX or Linux) is to use pip:

$ pip install abstar

If you don’t have pip, the Anaconda Python distribution contains pip along with a ton of useful scientific Python packages and is a great way to get started with Python.

abstar does not run natively on Windows, but Windows users can run abstar with Docker:

$ docker pull briney/abstar
$ docker run -it briney/abstar

Stable and development versions of abstar can also be downloaded from Github. You can manually install the latest development version of abstar with:

$ git clone https://github.com/briney/abstar
$ cd abstar/
$ python setup.py install

Note

If installing manually via setup.py and you don’t already have scikit-bio installed, you may get an error when setuptools attempts to install scikit-bio. This can be fixed by first installing scikit-bio with pip:

$ pip install scikit-bio

and then retrying the manual install of abstar. Starting with version 0.5, scikit-bio dropped support for Python 2.7, so install scikit-bio on Python 2.7 with:

$ pip install scikit-bio<=0.4.2

Requirements¶

Python 2.7 or 3.5+
abutils
biopython
celery
pymongo
pytest
scikit bio

Optional dependencies¶

Several optional abstar components have additional dependencies:

abstar.preprocessing requires FASTQC, cutadapt and sickle
sequence merging requires PANDAseq
downloading data from BaseSpace requires the BaseSpace Python SDK
batch_mongoimport requires MongoDB

If using Docker, all of the the optional dependencies are included.